feat: enable index resumption and enforce directory creation

The command now supports reopening existing indexes instead of failing when the output file exists. Control flow branches between opening an existing index and constructing a new one, moving configuration setup exclusively to the creation path. Directory existence is enforced upfront with proper I/O error propagation. The --force flag retains its original semantics by removing the target directory before proceeding with a fresh build.

DevDoc/implementation/filtering/index.html

@@ -733,14 +733,14 @@
   
   
     <li class="md-nav__item">
-      <a href="../obilayeredmap/" class="md-nav__link">
+      <a href="../layer_tier/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    obilayeredmap crate
+    obikindex layer tier
   
 
     
@@ -1236,6 +1236,34 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../partition_layer_cache/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Partition and layer caching (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -2158,7 +2186,7 @@ obikmer<span class="w"> </span>phylo<span class="w"> </span>myindex<span class="
 <h2 id="implementation">Implementation</h2>
 <ul>
 <li>
-<p><strong><code>obikpartitionner::filter::GroupQuorumFilter</code></strong> — implements <code>KmerFilter</code>
+<p><strong><code>obikindex::partition::filter::GroupQuorumFilter</code></strong> — implements <code>KmerFilter</code>
   using pre-computed ingroup and outgroup index vectors. The heavy logic
   (predicate parsing, three-value evaluation, genome classification) happens
   once before any iteration; each k-mer row evaluation is a simple index
@@ -2171,7 +2199,7 @@ obikmer<span class="w"> </span>phylo<span class="w"> </span>myindex<span class="
   list.</p>
 </li>
 <li>
-<p><strong><code>obikpartitionner::KmerPartition::iter_partition_kmers</code></strong> — accepts
+<p><strong><code>obikindex::partition::KmerPartition::iter_partition_kmers</code></strong> — accepts
   <code>filters: &amp;[Box&lt;dyn KmerFilter&gt;]</code> and applies them per-kmer before invoking
   the callback. <code>filter</code>, <code>dump</code>, and <code>unitig</code> all go through this single
   entry point.</p>